Sequence
atgc intronic sequence ATGC exonic sequencegtgagttgaaagcgatatatcccttgtggcagtcttaacatgtgtgcatagagttctaaaactttattgttttaaatttgttgcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53430.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA06G13330.1 (Glycine max), 3'ss of exon 21
gtgagttgaaagcgatatatc--cctt---gtggca-----gtcttaacat-gtgtgcatagagttctaaaactttattgttttaaatttgt---tgcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
||||||| | | ||| || |||| ||||| ||| | | || | | | ||| | || || | || || |||| |||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| ||||| || || || |||||
gtgagttaattcccctatgtctgccttttaatggcacactggtcatcatattatttatgtcatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATAAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: GLYMA04G41500.1 (Glycine max), 3'ss of exon 21
gtgagttgaaagcgatatatc--ccttgtggcag-----------tcttaacatgtgtgcatagagttctaaaactttattgttttaaatttg---ttgcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
||||||| | | ||| || ||| | ||| || || || | | | ||| | || || | || || ||| ||||||||||||||||| ||||| ||||| ||||| ||||| || || ||||||||||| ||||| || || || |||||
gtgagttaattcctctatgtctgcctattaacagcacactggtcatcatattatttatatgttatgttatcaacctaaaatgccctactcttgtctttgcagCTGTTTAAGATTAGTGAAGAAGTGGTGGTAGATGCCACTGATAAAGGGAATATAGCTCGGCTGATTAATCATTCT
upper sequence: AT5G53430.1 (Arabidopsis thaliana), 3'ss of exon 20
lower sequence: Vv16s0098g00350.t01 (Vitis vinifera), 3'ss of exon 21
----------------------------------gtgagttgaaagcgatatatcccttgtggcagtcttaacatgtgtgcatagagttctaaaactttattgttttaaatttgtt-gcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
| ||| | | | | || || | | | || |||| ||||| | |||| | | | |||| |||||| |||||||||||||| ||||| || || ||||| ||||| ||||| || ||||| || ||||| ||||| |||
gtgagaatctttctctttctttgtgttctaaaaagaccaccaaaaacaaccaaaacttttacatttcctcatctttcttg---agagcattaaaa-taaattgatattgttgtgtttgcagCTCTTTAAGATCAGTGAAGAAGTGGTAGTCGATGCTACAGATAAAGGAAACATTGCCCGCCTAATCAACCACTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcttaacatgtgtgcatagagttctaaaactttattgttttaaatttgttgcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
ttctaaa putative branch site (score: 2)
ttctaaaactttattg TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttgaaagcgatatatcccttgtggcagtcttaacatgtgtgcatagagttctaaaactttattgttttaaatttgttgcagCTGTTTAAGATCAGTGAGGAAGTAGTGGTGGATGCGACAGAGAAAGGGAATATTGCTCGACTAATAAACCATTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA